Buggy code:
@ Description ( "Conversion<seq2seq4repair_space>graph<seq2seq4repair_space>based<seq2seq4repair_space>around<seq2seq4repair_space>the<seq2seq4repair_space>clonal<seq2seq4repair_space>frame." ) @ Citation ( "Tim<seq2seq4repair_space>Vaughan,<seq2seq4repair_space>Alexei<seq2seq4repair_space>Drummod<seq2seq4repair_space>and<seq2seq4repair_space>Nigel<seq2seq4repair_space>French,<seq2seq4repair_space>" + ( "'Phylogenetic<seq2seq4repair_space>inference<seq2seq4repair_space>for<seq2seq4repair_space>bacteria<seq2seq4repair_space>in<seq2seq4repair_space>BEAST<seq2seq4repair_space>2'.<seq2seq4repair_space>" + "In<seq2seq4repair_space>preparation." ) ) public class ConversionGraph extends Tree { public Input < Alignment > alignmentInput = In . create ( "alignment" , "Sequence<seq2seq4repair_space>alignment<seq2seq4repair_space>corresponding<seq2seq4repair_space>to<seq2seq4repair_space>graph." ) ; public Input < Integer > sequenceLengthInput = new In < Integer > ( "sequenceLength" , "Sequence<seq2seq4repair_space>length.<seq2seq4repair_space>Alternative<seq2seq4repair_space>to<seq2seq4repair_space>providing<seq2seq4repair_space>full<seq2seq4repair_space>alignment." ) . setXOR ( alignmentInput ) ; public Input < String > fromStringInput = In . create ( "fromString" , "Initialise<seq2seq4repair_space>ARG<seq2seq4repair_space>from<seq2seq4repair_space>string<seq2seq4repair_space>representation." ) ; protected int sequenceLength ; protected List < Conversion > convs ; protected List < Conversion > storedConvs ; protected RegionList regionList ; protected CFEventList cfEventList ; protected ACGEventList acgEventList ; @ Override public void initAndValidate ( ) throws Exception { } public int getSequenceLength ( ) { } public void addConversion ( Conversion conv ) { } public void deleteConversion ( Conversion conv ) { } public List < Conversion > getConversions ( ) { } public int getConvCount ( ) { } public List < Region > getRegions ( ) { } public int getRegionCount ( ) { } public List < CFEventList . Event > getCFEvents ( ) { } public List < ACGEventList . Event > getACGEvents ( ) { } public double getClonalFrameLength ( ) { } public int getClonalFrameSiteCount ( ) { } public boolean isValid ( ) { <START_BUG> for ( int ridx = 1 ; ridx < ( convs . size ( ) ) ; ridx ++ ) { <END_BUG> if ( ! ( convs . get ( ridx ) . isValid ( ) ) ) return false ; if ( ( ( ( ( convs . get ( ridx ) . getStartSite ( ) ) < 0 ) || ( ( convs . get ( ridx ) . getStartSite ( ) ) >= ( getSequenceLength ( ) ) ) ) || ( ( convs . get ( ridx ) . getEndSite ( ) ) < 0 ) ) || ( ( convs . get ( ridx ) . getEndSite ( ) ) >= ( getSequenceLength ( ) ) ) ) return false ; } return true ; } @ Override public String toString ( ) { } public void fromString ( String str ) { } @ Override public void fromXML ( final Node node ) { } @ Override public ConversionGraph copy ( ) { } @ Override public void assignFrom ( StateNode other ) { } @ Override public void assignFromFragile ( StateNode other ) { } public String getExtendedNewick ( boolean includeRegionInfo ) { } private String extendedNewickTraverse ( beast . evolution . tree . Node node , boolean includeRegionInfo ) { } @ Override protected void store ( ) { } @ Override public void restore ( ) { } @ Override public void startEditing ( Operator operator ) { } @ Override public void init ( PrintStream out ) throws Exception { } @ Override public void log ( int nSample , PrintStream out ) { } @ Override public void close ( PrintStream out ) { } }

Fix:
for ( int ridx = 0 ; ridx < ( convs . size ( ) ) ; ridx ++ ) {